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Here we see a highly simplified animation of Groundskeeper Willie's Mouth. Here, the flesh folds from the outside to the inside, like a regular human. Most of the inside of the mouth is dark and cannot be seen, but some of it is exposed to the light, this can be seen on pratically every character on the Simpsons, as they all have an inside lip. Beard theory suggests that the beard attached to the outside area of skin folds itself into the mouth, thus consealing the only visible part of the inside mouth. Because of this, the inside lip now is covered by the beard and appears, in this case, red. Although not shown in this animation, I think the beard folding into the mouth is caused by the jaw, they act in conjunction with one another. As the jaw is lowered, the beard falls into the mouth, and when the jaw is raised again the beard flops out again.

One thing to point out is that the diagram has been heavily exaggerated for sake of effect. When I say the beard folds into the mouth, I don't literally mean the beard is like a piece of foam attached to the lip that literally folds in, the effect is far more subtle.

The dark yellow represents the part that you would not see as its in the mouth and thus not exposed to the light.